Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

Nature ◽  
2003 ◽  
Vol 422 (6930) ◽  
pp. 433-438 ◽  
Author(s):  
John E. Bowers ◽  
Brad A. Chapman ◽  
Junkang Rong ◽  
Andrew H. Paterson
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Evolution ◽  
Duplication Events ◽  
Chromosomal Duplication ◽  
Angiosperm Genome

scholarly journals Molecular Phylogenetic Analysis of the AIG Family in Vertebrates

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1190
Author(s):  
Yuqi Huang ◽  
Minghao Sun ◽  
Lenan Zhuang ◽  
Jin He
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Functional Characterization ◽  
Vertebrate Evolution ◽  
Molecular Phylogenetic Analysis ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Molecular Phylogenetic ◽  
Duplication Events ◽  
Inducible Genes

Androgen-inducible genes (AIGs), which can be regulated by androgen level, constitute a group of genes characterized by the presence of the AIG/FAR-17a domain in its protein sequence. Previous studies on AIGs demonstrated that one member of the gene family, AIG1, is involved in many biological processes in cancer cell lines and that ADTRP is associated with cardiovascular diseases. It has been shown that the numbers of AIG paralogs in humans, mice, and zebrafish are 2, 2, and 3, respectively, indicating possible gene duplication events during vertebrate evolution. Therefore, classifying subgroups of AIGs and identifying the homologs of each AIG member are important to characterize this novel gene family further. In this study, vertebrate AIGs were phylogenetically grouped into three major clades, ADTRP, AIG1, and AIG-L, with AIG-L also evident in an outgroup consisting of invertebrsate species. In this case, AIG-L, as the ancestral AIG, gave rise to ADTRP and AIG1 after two rounds of whole-genome duplications during vertebrate evolution. Then, the AIG family, which was exposed to purifying forces during evolution, lost or gained some of its members in some species. For example, in eutherians, Neognathae, and Percomorphaceae, AIG-L was lost; in contrast, Salmonidae and Cyprinidae acquired additional AIG copies. In conclusion, this study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, which can be employed for future functional characterization of AIGs.

scholarly journals Two Chimeric Chromosomes of Streptomyces coelicolor A3(2) Generated by Single Crossover of the Wild-Type Chromosome and Linear Plasmid SCP1

2004 ◽  
Vol 186 (19) ◽  
pp. 6553-6559 ◽  
Author(s):  
Masayuki Yamasaki ◽  
Haruyasu Kinashi
Keyword(s):  
Genome Evolution ◽  
Streptomyces Coelicolor ◽  
Linear Plasmid ◽  
Nucleotide Sequencing ◽  
Inverted Repeats ◽  
Wild Type ◽  
Linear Chromosome ◽  
Terminal Inverted Repeats ◽  
Type Chromosome ◽  
Chromosomal Duplication

ABSTRACT Streptomyces coelicolor A3(2) strain 2106 carries a 1.85-Mb linear plasmid, SCP1′-cysD, in addition to a 7.2-Mb linear chromosome. Macrorestriction analysis indicated that both linear DNAs are hybrids of the wild-type chromosome and the linear plasmid SCP1 on each side. Nucleotide sequencing of the fusion junctions revealed no homology between the recombination regions. SCP1′-cysD contains an SCP1 telomere and a chromosomal telomere at each end and therefore does not have terminal inverted repeats. In addition, SCP1′-cysD could not be eliminated from strain 2106 by various mutagenic treatments. Thus, we concluded that both the 7.2-Mb chromosome and SCP1′-cysD are chimeric chromosomes generated by a single crossover of the wild-type chromosome and SCP1. This may be regarded as a model of chromosomal duplication in genome evolution.

scholarly journals Mechanisms of Gene Duplication and Translocation and Progress towards Understanding Their Relative Contributions to Animal Genome Evolution

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Olivia Mendivil Ramos ◽  
David E. K. Ferrier
Keyword(s):  
Gene Duplication ◽  
Genome Evolution ◽  
Sequence Data ◽  
Genetic Material ◽  
Genetic Change ◽  
Genome Organisation ◽  
Base Pairs ◽  
Duplication Events ◽  
Major Route ◽  
Animal Genomes

Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence data that are becoming available, our understanding of the extent of duplication is greatly improving, both in terms of the scales of duplication events as well as their rates of occurrence. An accurate understanding of these processes is vital if we are to properly understand important events in evolution as well as mechanisms operating at the level of genome organisation. Here we will focus on duplication in animal genomes and how the duplicated sequences are distributed, with the aim of maintaining a focus on principles of evolution and organisation that are most directly applicable to the shaping of our own genome.

scholarly journals The First Evidence of a Host-to-Parasite Mitochondrial Gene Transfer in Orobanchaceae

2017 ◽  
Vol 59 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Dagmara Kwolek ◽  
Magdalena Denysenko-Bennett ◽  
Grzegorz Góralski ◽  
Magdalena Cygan ◽  
Patryk Mizia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Mitochondrial Genome ◽  
Genome Evolution ◽  
Horizontal Transfer ◽  
Mitochondrial Gene ◽  
Genetic Material ◽  
Parasitic Plants ◽  
Mitochondrial Genes ◽  
Mitochondrial Genome Evolution

AbstractSeveral parasitic plants are known to have acquired mitochondrial genes via a horizontal transfer from their hosts. However, mitochondrial gene transfer in this direction has not yet been found in the parasite-rich family Orobanchaceae. Based on a phylogenetic analysis of the mitochondrialatp6gene in selected species ofOrobanches.l., we provide evidence of a host-to-parasite transfer of this gene inO. coerulescens, which is a Eurasiatic species that parasitisesArtemisia(Asteraceae). We did not find the originalOrobanche atp6gene in this species, which suggests that it has been replaced by a gene that was acquired from Asteraceae. In addition, our data suggest the occurrence of a second HGT event in theatp6sequence – from Asteraceae toPhelipanche. Our results support the view that the transfer of genetic material from hosts to parasites influences the mitochondrial genome evolution in the latter.

Phylogenetic analysis and biogeography of Aegean taxa of the genus Dendarus (Coleoptera: Tenebrionidae)

2003 ◽  
Vol 34 (3) ◽  
pp. 295-312 ◽  
Author(s):  
◽  
◽  
◽  
Keyword(s):  
Phylogenetic Analysis ◽  
Strong Support ◽  
Component Analysis ◽  
Aegean Islands ◽  
Duplication Events ◽  
History Of ◽  
Tree Length ◽  
Species Groups ◽  
The Mediterranean Basin ◽  
Coleoptera Tenebrionidae

AbstractThe genus Dendarus Latr. is distributed throughout the Mediterranean basin with numerous species in the Aegean islands. This paper presents a phylogenetic analysis and the biogeography of most taxa present in the area. Phylogenetic analysis of two outgroup and 25 ingroup taxa based on adult morphology, including 50 characters and 119 character states, produced two equally parsimonious trees (tree length = 148, C.I. = 0.42, R.I. = 0.70, R.C. = 0.294). These trees provide strong support for the monophyly of Dendarus and also define four species groups: the foraminosus group, present mainly on the island of Crete; the rhodius group, present in Dodecanese islands, the sinuatus group present in the central Aegean islands, and another group consisting of taxa from mainland Greece (D. messenius, D. caelatus, D. tenellus, and D. plicatulus paganettii). All area cladograms produced by Compatibility Component Analysis, Brooks Parsimony Analysis, and especially by Component Analysis, correspond quite closely to the hypothesized palaeogeographic history of the studied area and therefore partly support the idea of a vicariant evolution of Dendarus taxa in this region. We distinguished certain monophyletic groups distributed (with some exceptions) within well-defined geographical and palaeogeographical regions of the Aegean. However, we found certain inconsistencies (with Reconciled Tree Analysis) that are probably the result of dispersal, extinction, or duplication events that are independent of the sequence of vicariance events.

scholarly journals OrthoFinder: phylogenetic orthology inference for comparative genomics

2018 ◽  
Author(s):  
David M. Emms ◽  
Steven Kelly
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Gene Duplication ◽  
Phylogenetic Inference ◽  
High Accuracy ◽  
Comparative Genomic ◽  
Heuristic Methods ◽  
Major Advance ◽  
Inference Method ◽  
Duplication Events

AbstractHere, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted genes trees, gene duplication events, the rooted species tree, and comparative genomic statistics. Each output is benchmarked on appropriate real or simulated datasets and, where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available athttps://github.com/davidemms/OrthoFinder.

scholarly journals Evolutionary contribution of duplicated genes to genome evolution in the ginseng species complex

2021 ◽  
Author(s):  
Ming-Rui Li ◽  
Ning Ding ◽  
Tianyuan Lu ◽  
Jing Zhao ◽  
Zhen-Hui Wang ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Species Complex ◽  
Cytosine Methylation ◽  
Functional Enrichment ◽  
Small Scale ◽  
Nucleotide Variation ◽  
Duplicated Genes ◽  
Evolutionary Patterns ◽  
Genome Wide ◽  
Duplication Events

Abstract Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains under-investigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome and proteome datasets. Our genome-wide comparative analyses revealed that while the ginseng species complex were recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypo-methylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hyper-methylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.

Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae

2007 ◽  
Vol 43 (3) ◽  
pp. 1066-1075 ◽  
Author(s):  
Nan Wang ◽  
Pierre F. Baldi ◽  
Brandon S. Gaut
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Evolution ◽  
Gene Gain
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